# BUSCO plots all kmer sets
# setwd("~/Desktop/R/ramon/TransPi/paper/")
library(reshape2)
library(plotly)
library(dplyr)
csv=read.csv("busco3_50.csv", header=TRUE)
Complete
## Complete genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Single
## Single genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Kruskal-Wallis test was significant (p<.05)"
##
## Pairwise comparisons using Wilcoxon rank sum test
##
## data: sing$Score and sing$Program
##
## Transpi
## Trinity 3.9e-05
##
## P value adjustment method: BH
Duplicated
## Duplicated genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Kruskal-Wallis test was significant (p<.05)"
##
## Pairwise comparisons using Wilcoxon rank sum test
##
## data: dup$Score and dup$Program
##
## Transpi
## Trinity 8e-07
##
## P value adjustment method: BH
Fragmented
## Fragmented genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Kruskal-Wallis test was significant (p<.05)"
##
## Pairwise comparisons using Wilcoxon rank sum test
##
## data: frag$Score and frag$Program
##
## Transpi
## Trinity 7.9e-06
##
## P value adjustment method: BH
Missing
## Missing genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Only TransPi
Complete
## Complete genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Single
## Single genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Duplicated
## Duplicated genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Fragmented
## Fragmented genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Missing
## Missing genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Complete
## Complete genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.022 0.01083 0.097 0.908
## Residuals 33 3.686 0.11169
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = ceTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA -0.05833333 -0.3931241 0.2764574 0.9044460
## KmerC-KmerA -0.04166667 -0.3764574 0.2931241 0.9499673
## KmerC-KmerB 0.01666667 -0.3181241 0.3514574 0.9918091
Single
## Single genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.052 0.0258 0.041 0.96
## Residuals 33 21.028 0.6372
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = ceTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA -0.03333333 -0.8329982 0.7663315 0.9942497
## KmerC-KmerA 0.05833333 -0.7413315 0.8579982 0.9825010
## KmerC-KmerB 0.09166667 -0.7079982 0.8913315 0.9573793
Duplicated
## Duplicated genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.065 0.0325 0.081 0.923
## Residuals 33 13.282 0.4025
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = ceTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA -0.025 -0.6605438 0.6105438 0.9948775
## KmerC-KmerA -0.100 -0.7355438 0.5355438 0.9213138
## KmerC-KmerB -0.075 -0.7105438 0.5605438 0.9548928
Fragmented
## Fragmented genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Missing
## Fragmented genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.0117 0.00583 0.083 0.921
## Residuals 33 2.3183 0.07025
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = ceTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA 0.041666667 -0.2238511 0.3071844 0.9217148
## KmerC-KmerA 0.008333333 -0.2571844 0.2738511 0.9967358
## KmerC-KmerB -0.033333333 -0.2988511 0.2321844 0.9491153
BUSCO and reads
## comp.Program comp.Category comp.Score comp.Reads comp.Sample
## 1 Transpi Complete 85.5 24,017,399 CE1
## 2 Transpi Complete 85.3 24,409,279 CE2
## 3 Transpi Complete 85.3 24,694,386 CE3
## 4 Transpi Complete 85.7 26,159,433 CE4
## 5 Transpi Complete 85.4 26,417,070 CE5
## 6 Transpi Complete 85.2 24,711,402 CE6
Complete
## Complete genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Single
## Single genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0 0.24 0.003 0.997
## Residuals 51 4117 80.72
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = dmTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA -0.22222222 -7.451660 7.007215 0.9969692
## KmerC-KmerA -0.05555556 -7.284993 7.173882 0.9998103
## KmerC-KmerB 0.16666667 -7.062771 7.396104 0.9982940
Duplicated
## Duplicated genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Fragmented
## Fragmented genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Missing
## Missing genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
BUSCO and reads
## comp.Program comp.Category comp.Score comp.Reads comp.Sample
## 1 Transpi Complete 44.7 15,648,174 DM1
## 2 Transpi Complete 44.6 15,181,806 DM2
## 3 Transpi Complete 37.0 9,857,308 DM3
## 4 Transpi Complete 39.8 15,940,368 DM4
## 5 Transpi Complete 48.5 18,874,930 DM5
## 6 Transpi Complete 35.1 21,169,448 DM6
Complete
## Complete genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.02 0.0102 0.005 0.995
## Residuals 39 80.18 2.0558
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = mmTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA 0.042857143 -1.277442 1.363156 0.9965582
## KmerC-KmerA 0.050000000 -1.270299 1.370299 0.9953184
## KmerC-KmerB 0.007142857 -1.313156 1.327442 0.9999042
Single
## Single genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Duplicated
## Duplicated genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Fragmented
## Fragmented genes comparison
## [1] "One (or more) set is not normally distributed"
## [1] "Data not significant. Skipping pairwise comparison"
Missing
## Missing genes comparison
## [1] "All sets are normally distributed"
## [1] "ANOVA"
## Df Sum Sq Mean Sq F value Pr(>F)
## Kmer 2 0.078 0.0388 0.089 0.915
## Residuals 39 17.079 0.4379
## [1] "Pairwise comparison"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Score ~ Kmer, data = mmTra2)
##
## $Kmer
## diff lwr upr p adj
## KmerB-KmerA -0.10000000 -0.7093637 0.5093637 0.9158524
## KmerC-KmerA -0.07857143 -0.6879351 0.5307923 0.9471300
## KmerC-KmerB 0.02142857 -0.5879351 0.6307923 0.9959619
BUSCO and reads
## comp.Program comp.Category comp.Score comp.Reads comp.Sample
## 1 Transpi Complete 96.9 33,540,466 MM1
## 2 Transpi Complete 96.4 43,541,512 MM2
## 3 Transpi Complete 97.0 43,440,008 MM3
## 4 Transpi Complete 95.8 33,595,655 MM4
## 5 Transpi Complete 95.0 33,174,108 MM5
## 6 Transpi Complete 95.5 35,030,665 MM6